The Neuroscience of Mindfulness: How Meditation Changes Your Brain
Adapted from an article by Brian Penny, a former heroin addict who overcame addiction and became a neuroscientist and mindfulness practitioner.
I spent most of my life thinking about the past and the future. My mind was torn by doubts, I was constantly worried, but I didn’t understand the source of my suffering. To numb the pain, I turned to drugs, which led to fifteen years of chronic heroin addiction. The drug pushed me to the brink, but I got lucky. The worst night of my life forced me to quit, and after that, I saw the world in a new way.
In October 2013, I was introduced to the concept of mindfulness. Since then, I’ve been drug-free, became an author, a lecturer, and started a PhD at Ireland’s second most prestigious university.
Understanding the science behind mindfulness and meditation can be very helpful for those just starting out. Knowledge of brain neurophysiology is especially useful for people who want to evaluate the potential results of developing new habits. (Gretchen Rubin calls these people “questioners.”)
How the Brain Works
Neurons
Neurons are the basic building blocks of the brain. We have about 86 billion of them. Each neuron fires five to fifty times per second. On average, each neuron has over 5,000 connections to other neurons. As you read this sentence, billions of neurons are transmitting signals in your head—a very complex system.
Neurons allow us to feel and record the experience of every action, thought, and sensation we’ve ever had. This is how we learn, biologically. The more you repeat a certain behavior—like practicing mindfulness or worrying—the more you strengthen the connections between specific neurons.
Neural connections become more active, transmit signals faster, and are used more often. To save energy, the brain creates new structures for specific tasks. This is how we learn new things, using what scientists call the brain’s neuroplasticity.
Neuroplasticity
Our brain is very malleable, like clay; our life experiences shape its structure and form. This process is much like physical exercise. For example, thirty reps at the gym won’t make your muscles stronger, but thirty reps every day for a year can have that effect. The same is true for the brain: over time, its shape changes.
As someone who was always anxious, I constantly felt tension, anxiety, and worry. If my brain wasn’t scanning the environment for threats, it was looking for ways to cope with anxiety. I turned my brain into a well-oiled worry machine.
The same goes for other negative feelings, thoughts, and emotions. Whatever arises inside you—anger, self-doubt, or fear—your brain will reflect it in its structure.
The Reptilian Brain
The human brain can be divided into three areas: the reptilian brain, the limbic system, and the cortex.
The reptilian brain is the oldest part, evolutionarily speaking. It controls vital functions like body temperature, heart rate, and breathing. This structure manages our instincts and drive for self-preservation, ensuring the survival of the species.
This primitive part of the brain is responsible for our reckless and impulsive actions, which often cause serious problems in life. The need to survive is so strong that it can lead to a conflict between the reptilian brain and the cortex, which is responsible for logical behavior.
It’s like two people arguing: “Will you drink?” “No, I’ll pass!” “Are you sure you want to?” “Yes, but I’ll regret it later!” If you’re an anxious person like me, the reptilian brain may interpret anxiety as a threat it doesn’t understand.
From experience, I learned that alcohol could temporarily ease my anxiety. So when I agreed to drink, the reptilian brain won. I often recall my years in addiction, when my impulsive behavior was driven by this part of the brain. There was no struggle, just total surrender—the “crocodile” always got its drugs.
The Limbic System
The limbic system consists of several structures above the reptilian brain. The main components are the hippocampus, amygdala, and hypothalamus.
The limbic system supports many functions. The hippocampus is responsible for forming memories. The nearby amygdala plays a key role in emotions like fear, anxiety, or anger. It also determines the vividness of our memories, which is why emotional memories are usually the strongest.
The hypothalamus connects the brain to the endocrine system and helps us respond to stress. It sends chemical signals that stimulate or inhibit the production of hormones that help us cope with tension.
The Cerebral Cortex
Of the three regions, the cortex appeared last in evolution. It consists of gray matter surrounding the deeper white matter of the brain’s hemispheres. Gray matter contains neuron bodies, while white matter connects several gray areas with fibers.
The cortex is involved in higher-order activities: abstract thinking, problem-solving, risk assessment, and speech. This flexible structure gives humans learning abilities unmatched in nature. Thanks to the cortex, humans can do things no other species can.
Stress Response
During stress, the three main structures of the limbic system—the hippocampus, amygdala, and hypothalamus—work together.
Here’s how it works in real life. You’re standing in a field and notice something that looks like a snake. Memories in the hippocampus tell you that you’re afraid of snakes. This activates the amygdala—the brain’s fear center—which in turn stimulates the hypothalamus.
The hypothalamus sends signals to the pituitary gland, which relays information to the adrenal glands, releasing cortisol into the bloodstream. Cortisol is the main stress hormone, preparing the body to fight or flee.
Automatic Neurophysiology: It’s Not Life or Death
The cortex, reptilian brain, and limbic system work together. They’re connected by complex neural pathways (white matter) and constantly influence each other.
In the snake example, the reptilian brain’s survival instinct activated the limbic system, releasing cortisol into the body. This instant, hardwired reflex could save you from sudden danger.
At the same time, the rational part of the brain—the cortex—was assessing the situation. This is a slower process, and if you’re lucky, the “snake” turns out to be just a piece of hose. Once you realize this, the cortex deactivates the amygdala, which then limits cortisol release via the hypothalamus, returning your body to a balanced state (homeostasis).
This is a simple example, but in real life, things are rarely so clear-cut—especially in our overloaded world. When I think about how brain neurophysiology relates to my chronic anxiety and destructive addiction, my head starts to hurt. But let’s try to figure it out together.
My anxiety was the result of childhood trauma, rooted in bodily sensations. From a young age, I was terrified by my own heartbeat, breathing, or pulse. If someone suggested listening to my heartbeat, or I just talked about it, my amygdala would light up like a Christmas tree.
My reptilian brain, focused on self-preservation, would say: “I’ll get you out of this nightmare, buddy.” What did I do? Anything to escape myself, anything to calm my overactive brain—for me, that meant drugs.
I wondered what my rational mind, the cortex, was doing during all this. After all, a heartbeat is normal. I was never in real danger. Of course, my logical brain knew this. Shouldn’t it have calmed the limbic system?
Neuroscientists have given me many theories that might answer this. The cortex may not be able to handle the overactivity of the limbic system, or it may fail to logically suppress irrational fears. The truth is, we don’t really know how it all works, but understanding the basics helped me realize there was nothing to worry about. It’s not a matter of life or death.
Emotional Hijacking
Have you ever been caught off guard by fear? I have, constantly! I couldn’t handle it before or during my addiction—I was afraid of everything. Daniel Goleman calls this “emotional hijacking,” when your amygdala screams like a siren.
This happens when something in your environment causes stress. For example, your partner raises their voice, a coworker criticizes you, you narrowly avoid a car accident, or someone startles you.
From a neurophysiological perspective, the visual and auditory areas of the cortex—depending on the stimulus—send messages to the amygdala, which triggers the stress response.
This is how most people handle tension; this reaction is the pinnacle of our species’ evolution. But in today’s world, stress is more often caused by our own thoughts than by external triggers.
There are two types of internal stress: obsessive thoughts about the unchangeable past and fantasies about the future. These internal stressors are the worst triggers. What happens around us is variable, but the struggle with our own thoughts is constant. When it comes to stress, it’s like a leaky cortisol faucet… you hear the steady drip, drip, drip.
Mindful Neurophysiology
If you’re constantly anxious, angry, or self-loathing, your brain will eventually reflect these experiences in its structure. But the opposite is also true: you can direct your thoughts in a more positive direction and literally reshape your brain.
By regularly practicing neuroplasticity through mindfulness, you can become more resilient to stressors, develop sharper focus, and manage your emotions more effectively.
Below are images of my brain. The left scan was part of a study in 2013, on my second “clean” day after 15 years of addiction. The right scan was taken in May 2018 for a documentary about stress.
My brain was so different that the person analyzing it couldn’t visually compare the standard markers (see above for a more technical explanation).
It’s still hard to say what caused such dramatic changes. Four and a half years passed between scans, and I changed many aspects of my life, including diet, exercise, and sleep. I went back to college and, of course, stopped using heroin.
But I can see for myself that my brain’s transformation was the result of developing mindfulness. Everything changed when I learned about mindfulness. I was given a tool to defeat my worst enemy—anxiety—and it changed everything.
Managing Emotions
Research shows that regular mindfulness practice weakens the amygdala’s ability to hijack your emotions. There are at least two reasons for this. First, the amygdala itself shrinks in size. Second, the connection between the amygdala and the fear-related parts of the cortex weakens. Meanwhile, connections between the cortex and areas involved in higher-level activities (like self-awareness) are strengthened.
Mindfulness practice gave me both of these gifts. I literally shrank the fear center of my brain, and as a result, I stopped being afraid and anxious for no reason. Stress still gets me going, but because there’s now a space between stimulus and response, my mind is no longer hijacked by emotions.
Attention and Focus
Our attention is managed by the anterior cingulate cortex. It’s also linked to self-determination and mental flexibility—natural enemies of obsessive thoughts and rigid thinking.
Researchers have found an increase in the size of this brain area after meditation practice. More importantly, when the connection between the amygdala and the cortex weakens (meaning the area responsible for emotional hijacking loses control), it becomes easier to manage attention.
One study found that practicing mindfulness for twenty minutes a day over five days improved concentration, and a later study reported that even brief mindfulness practice improves attention, even for beginners.
Self-Awareness
“Identity” is your sense of self—how you see yourself. If you suffer from something, like I did with anxiety, disconnecting from your “identity” can bring inner relief.
Self-awareness developed through mindfulness techniques can separate you from your “identity.” Instead of letting your self-image control you, you can step back: observe or know yourself as if from the outside.
Although research in this area is just beginning, some very telling findings have already been made about the brain’s default mode network.
The brain switches to default mode when you have no specific task: you drift from one thought to another. This mode influences deep rumination and overthinking, which are very harmful to our well-being.
Mindfulness reduces the activation of the default mode network, and as a result, calms our minds. In one study, activity in the brain regions responsible for the default mode was lower in people who practiced meditation compared to those who didn’t. Scientists found that meditators were less prone to self-absorption.
Simple Steps That Lead to Results
We often think of psychological phenomena like stress, rumination, and anxiety as abstract concepts that can’t be touched, felt, or seen. But in reality, all of this is directly connected to our biology.
Fortunately, mindfulness can help us deal with much of the suffering in the modern world. I struggled with anxiety and addiction for almost my entire life, and only mindfulness helped me return to a normal state.
By consistently practicing mindfulness, I didn’t just feel better—it physically changed the structure and state of my brain. I no longer feel anxious, I don’t worry, and I can focus more easily and deeply than ever before.
Bad habits are hard to break, but good ones are even harder. My anxiety was replaced by a sense of calm that’s now deeply embedded in my brain and has become my new normal.
Anyone can change the shape of their brain and improve their ability to think and feel. All it takes is consistent mindfulness practice. Just 10 minutes a day is enough.
My final request: do this every day. Building the habit is crucial if you want to change your brain, increase awareness, focus, and emotional control. I don’t think I’m asking too much.